3D complex: a structural classification of protein complexes.
3D complex: a structural classification of protein complexes.
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DOI：
10.1371/journal.pcbi.0020155
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发表时间：
2006-11-17
影响因子：
4.3
通讯作者：
Teichmann SA
中科院分区：
文献类型：
--
作者：
Levy ED;Pereira-Leal JB;Chothia C;Teichmann SA
细胞中的大多数蛋白质组装成复合物以执行其功能。因此，了解蛋白质的物理化学性质以及蛋白质之间相互作用的演变至关重要。蛋白质数据库是此类研究的重要信息来源，因为超过一半的结构是同源或异源蛋白质复合物。在这里，我们提出了已知的3-D结构的整个蛋白质复合物的第一个层次分类的基础上，代表他们的基本结构特征作为一个图形。这种分类提供了蛋白质数据库中所有复合物的第一个概述，并允许在不同的详细程度上推导出非冗余集。这表明，根据可接受的冗余水平，一半到三分之二的已知结构是多聚体。我们还分析了它们的子单元的拓扑排列方面的结构，并发现它们形成了一个小数目的安排相比，所有理论上可能的。这是因为大多数复合物含有四个或更少的亚基，并且大多数是同源的。此外，复合物中存在强烈的对称倾向，即使是异聚复合物也是如此。最后，通过比较蛋白质数据库中的生物单元与蛋白质四级结构数据库中的生物单元，我们发现了许多可能的四级结构归属错误。我们的分类，可作为一个数据库和Web服务器在http://www.3Dcomplex.org，将是一个起点，为未来的工作，旨在了解蛋白质复合物的结构和进化。在过去的十年中，数百万个基因的测序结果对应的蛋白质结构域或折叠的数量要少得多，可能只有几千个。由于结构数据正在以快速的速度积累，因此结构域的分类（如SCOP）有助于理解序列-结构关系。最近，相互作用结构域对的分类解决了序列趋异和结构域-结构域相互作用之间的关系。一个尚待研究的描述水平是蛋白质复合物水平，这是细胞内大多数蛋白质的生理相关状态。在这里，Levy和他的同事提出了一个蛋白质复合物的分类方案，这将有助于更好地理解它们的结构特性和进化。
Most of the proteins in a cell assemble into complexes to carry out their function. It is therefore crucial to understand the physicochemical properties as well as the evolution of interactions between proteins. The Protein Data Bank represents an important source of information for such studies, because more than half of the structures are homo- or heteromeric protein complexes. Here we propose the first hierarchical classification of whole protein complexes of known 3-D structure, based on representing their fundamental structural features as a graph. This classification provides the first overview of all the complexes in the Protein Data Bank and allows nonredundant sets to be derived at different levels of detail. This reveals that between one-half and two-thirds of known structures are multimeric, depending on the level of redundancy accepted. We also analyse the structures in terms of the topological arrangement of their subunits and find that they form a small number of arrangements compared with all theoretically possible ones. This is because most complexes contain four subunits or less, and the large majority are homomeric. In addition, there is a strong tendency for symmetry in complexes, even for heteromeric complexes. Finally, through comparison of Biological Units in the Protein Data Bank with the Protein Quaternary Structure database, we identified many possible errors in quaternary structure assignments. Our classification, available as a database and Web server at http://www.3Dcomplex.org, will be a starting point for future work aimed at understanding the structure and evolution of protein complexes. The millions of genes sequenced over the past decade correspond to a much smaller set of protein structural domains, or folds—probably only a few thousand. Since structural data is being accumulated at a fast pace, classifications of domains such as SCOP help significantly in understanding the sequence–structure relationship. More recently, classifications of interacting domain pairs address the relationship between sequence divergence and domain–domain interaction. One level of description that has yet to be investigated is the protein complex level, which is the physiologically relevant state for most proteins within the cell. Here, Levy and colleagues propose a classification scheme for protein complexes, which will allow a better understanding of their structural properties and evolution.
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